After stepping down as a Member of Parliament in 2006, Tan was appointed Executive Director and Deputy Chairman of the Government of Singapore Investment Corporation (GIC) and Chairman of Singapore Press Holdings Limited (SPH). He also served as Chairman of Singapore's National Research Foundation, and Deputy Chairman of the Research, Innovation and Enterprise Council.[2] In July 2011, he resigned from these positions to contest in the 2011 presidential election. He received 35.20% of the votes, winning by a narrow 0.34% margin over the second-placed candidate. Tan was sworn in as President on 1 September 2011.[3]

In 2005, Tan was presented the NUS Eminent Alumni Award in recognition of his role as a visionary architect of Singapore’s university sector.[4] In 2010, he was presented the inaugural Distinguished Australian Alumnus Award by the Australian Alumni Singapore (AAS) at its 55th anniversary dinner in recognition of his distinguished career, and his significant contribution to society and to the Australian alumni community.[7][8] In 2014, Tan was conferred an honorary doctorate by his Alma mater University of Adelaide for his “long record of outstanding achievements both as a leader in the Singapore government and in the business sectors.[9]

Singapore saw a leadership transition that started shortly before the 1984 general elections. Three months before the election, all the members of the PAP Central Executive Committee (CEC)—except Lee Kuan Yew —had left the CEC to allow the "second generation" of PAP leaders to take root. This leadership transition saw Tan replace Singapore's chief economic architect, Goh Keng Swee, as Education Minister.

Before the 1984 election, Lee Kuan Yew and Goh Keng Swee had also pushed for policies that experimented with eugenics in Singapore, including a policy that favoured children of more well-educated mothers ahead of children of less-educated mothers in primary school placement. However, in response to popular discontent and public criticism of the policy during and after the 1984 general election (which saw the lowest votes for the PAP since independence), Tan as the new Minister for Education announced that the scheme would be scrapped. This announcement followed Tan's own May 1985 recommendation to the Cabinet to scrap the scheme.[11][12]

As Minister for Trade and Industry, Tan was concerned about investors' reactions to a perceived deterioration of labour relations and the impact on foreign direct investment.

In his analysis, historian Michael Barr explains that older [grassroots] union leaders" bore "increasing disquiet" at their exclusion from consultation in NTUC's policies, which were effectively managed by "technocrats" in the government. Unlike the previous NTUC secretary-general Lim Chee Onn, Lee Kuan Yew's protégé Ong Teng Cheong in 1983 had an "implicit pact" with the trade unions—involving grassroots leaders in top decisions and "working actively and forcefully" in the interests of the unions "in a way Lim had never seen to do"—in exchange for the unions' continued "cooperation on the government's core industrial relations strategies". (In 1969 the NTUC had adopted "a cooperative, rather than a confrontational policy towards employers".)[13]

Although striking was prohibited and trade unions were barred from negotiating such matters as promotion, transfer, employment, dismissal, retrenchment, and reinstatement, issues that "accounted for most earlier labour disputes", the government provided measures for workers' safety and welfare, and serious union disputes with employers were almost always handled through the Industrial Arbitration Court, which had powers of both binding arbitration and voluntary mediation.[14] However, Ong felt these measures did not prevent "management [from] taking advantage of the workers", recalling in a 2000 interview in Asiaweek: "Some of them were angry with me about that... the minister for trade and industry [Tan] was very angry, his officers were upset. They had calls from America, asking what happened to Singapore?"[15] However the fact that the strike only lasted two days before "all the issues were settled" was cited by Ong in a 2000 interview with Asiaweek as proof that "management was just trying to pull a fast one".

Separately, Tan initially opposed the timing of building the Mass Rapid Transit in 1981 when it was raised by Ong. Tan held the view that the local construction industry was overheated at the time, and public housing should take priority.[16]

After Ong Teng Cheong and Lee Hsien Loong were diagnosed with cancer in 1992,[17] and 1993[18] Tan was asked[19] to return to Cabinet in August 1995 as Deputy Prime Minister (1995–2005) and Minister for Defence (1995–2003). It was reported that he declined an offer of make-up pay, which compensated ministers for a loss in salary when they leave the private sector.[20] Tan declared, "the interests of Singapore must take precedence over that of a bank and my own personal considerations".[21]

In August 2003, he relinquished the defence portfolio and became the Co-ordinating Minister for Security and Defence, while retaining the post of Deputy Prime Minister.[4] He later persuaded the Minister for National Development Mah Bow Tan to abandon plans to demolish an old mosque in his constituency of Sembawang.[22] Dubbed the “Last Kampung Mosque in Singapore”, it was later designated a heritage site.[23]

Tan joined other dissenting colleagues in opposing the implementation of “integrated resorts” with their attached casinos to Singapore. Commenting on an MCYS survey of gambling habits, Tan had said he was “appalled” that a newspaper headline dismissed the number of likely problem gamblers (55,000) as insignificant: “I don't think it's insignificant. Every Singaporean is important. Every Singaporean that gets into trouble means one family that is destroyed. It cannot be a matter of small concern to the Government.”[24][25]

Tan stepped down as Deputy Prime Minister and Co-ordinating Minister for Security and Defence on 1 September 2005. After his retirement from the Cabinet, Tan became the chairman of the National Research Foundation, and deputy chairman of the Research, Innovation and Enterprise Council. He was also the Executive Director of the Government of Singapore Investment Corporation (GIC), and Chairman of Singapore Press Holdings Limited (SPH).[2]

Tan's tenure at GIC coincided with moves towards "greater disclosure in the investment fund’s activities amid mounting concerns about the secretive fund's influence after high-profile investments in UBS and Citigroup."[26] In September 2008 GIC issued the first of a series of annual reports on GIC’s portfolio management, governance, and people.[27] In 2008 during the global financial crisis, GIC experienced a significant drop in its real rate of return which recovered[28] subsequently.

Tan has served as patron of many organisations, including the Singapore Dance Theatre,[29] the Singapore Computer Society,[30] SJI International,[31] the Duke-NUS Medical School,[32] and the MIT Club of Singapore.[33] Most recently, in May 2011, he was named as the first patron of Dover Park Hospice.[34]

On 22 December 2010, Tan announced that he would step down from his government-linked positions at GIC and SPH in order to run for the office of President of Singapore.[36] Tan's campaign stressed his independence and his divergent views from the PAP government in specific policies, citing a remark made by East Coast GRC MP Tan Soo Khoon in 2005: “It is probably the first time that I have heard Cabinet Ministers, starting with no less than the Deputy Prime Minister, Dr Tony Tan, expressing divergent views [on the Integrated Resorts question].”[37][38] However, competing presidential election candidates and former PAP members Tan Kin Lian and Tan Cheng Bock questioned Tan's independence from the party.[39] On 7 July 2011, Tony Tan submitted his presidential eligibility forms.[40]

On 29 July 2011, Tan responded to online allegations[41] that his son Patrick Tan had received preferential treatment during compulsory military service, officially known as National Service (NS) in Singapore. "My sons all completed their National Service obligations fully and I have never intervened in their postings," he said.[42][43] Tan also noted that he had served as Defence Minister from 1995 to 2003, while Patrick Tan said that it was in 1988 that he been permitted by Singapore's Ministry of Defence (MINDEF) to disrupt his NS for premedical studies in Harvard University[44] and an MD-PhD program in Stanford University under a President’s Scholarship and Loke Cheng Kim Scholarship.[45] MINDEF clarified that, prior to 1992, disruptions were allowed for overseas medical studies, and longer periods of disruption were granted for those admitted to universities in the United States, where medicine is a graduate course. American medical students are required to complete a "pre-medical component for a general undergraduate degree" before applying to medical school.[46] In response to a question in Parliament on the subject of deferments, Minister for Defence Ng Eng Hen stated on 20 October 2011 that Patrick Tan had not been given any special treatment.[47]

Describing himself as "Tested, Trusted, True", Tan said his past experiences will help him steer Singapore through the financial uncertainty lying ahead.[48]

On Nomination Day (17 August 2011), Tan unveiled his election symbol – a pair of black glasses which resembles the trademark spectacles he has steadfastly worn for years. His campaign materials, which included caps, postcards and fridge magnets also carried the symbol. About 9,400 posters and 200 banners were printed.[49] Many of these were later recycled to make bags produced by the fashion company Charles & Keith.[50]

Tan's presidential bid was endorsed by the 10,000-strong Federation of Tan Clan Associations on 7 August 2011.[51] By 13 August 2011, the leaders of 19 NTUC-affiliated unions (which have 128,000 members) had endorsed his bid.[52][53] On 14 August, the leadership of the Singapore Federation of Chinese Clan Associations (SFCCA) and the Singapore Chinese Chamber of Commerce & Industry (SCCCI) also endorsed his bid.[54][55] The leadership of another four unions from the construction and real estate sector, which represent more than 50,000 members, endorsed Tan's bid on 16 August. Nine Teochew clan associations also supported Tan.[56] Union leaders in three sectors – Transport and Logistics, Marine and Machinery-engineering, and Infocomm and Media – endorsed Tan on 17 August. They together represent 112,000 workers.[57] Tan received The Singapore Malay Chamber of Commerce and Industry (SMCCI) endorsed Tan's presidential candidacy on 18 August 2011. It is also was the first[58] Malay organisation to do so.

After a closed door meeting with the Singapore Malay Chamber of Commerce and Industry on 11 August 2011, Tan remarked that it is "not too early" for the government to have contingency plans in case an economic crisis hits Singapore, noting that "with his background and knowledge", he added that he was in a position to provide "a steady hand".[59]

Speaking to reporters after a dialogue with the Singapore Manufacturers' Federation the following day, Tan remarked that it would be a "grave mistake" to phase out manufacturing in Singapore, which has been transitioning to a service economy and an information economy since the 1980s. He then went on to describe manufacturing as a "key pillar of Singapore's economy". Without the sector, he feels Singapore's economy will be "less resilient, less diversified" and there will be "fewer options for our young people and Singapore will lose."[60]

On 15 August 2011, following the National Day Rally speech by Prime Minister Lee Hsien Loong, Tan said that one point he found particularly interesting in Lee's address was whether Singapore would remain pragmatic in its policy making, or if it would turn populist. He added that the temptation to make populist decisions was affecting the presidential election, "with some candidates appealing to the public in ways that could go beyond the parameters of the Singapore's Constitution".[61][62]

On 17 August 2011, crowds booed[63] at Tan and his son as he delivered his two-minute Nomination Day speech. According to The Straits Times, the jeers came from a vocal group of people who mostly supported another presidential candidate Tan Jee Say.[64] At a press conference later that day, Tony Tan said that while different points of view were to be expected in a campaign, it was disappointing to have people who would not even listen, and hoped that Singaporeans would listen to the views of all the candidates. He said, "I don't think that jeering or heckling is the right way to go about the campaign, particularly in a campaign for the president, which has to be conducted with decorum and dignity."[65]

On the first presidential candidate broadcast on 18 August 2011, while other candidates made promises in their first presidential candidate broadcasts on Thursday night, Tan refrained[66] from making promises during the broadcast and focused on the role of the President instead. Speaking in English, Chinese and Malay, Tan said,[67] "Some people argue that the President must take a public stand on current issues. I hear and share the concerns of Singaporeans. But policies are debated in Parliament and implemented by the Government. Others have said that the President must oppose the Government. That is a job for the Opposition. People interested in such roles should run for Parliament in the next General Election."

A key area in which Tan sought to distinguish his presidency was in promoting a more active civil society. Speaking in November 2013, he argued that Singapore needed to build up its “social reserves” to complement the substantial financial reserves the city state had accumulated over time.[68] An example of this, he said, was the way that he had expanded Singapore's President's Challenge charity event to go beyond fund-raising to promote volunteerism and social entrepreneurship.[69]

In October 2014, he made the first state visit of a Singaporean head of state to the United Kingdom.[70]